[gmx-users] Polarizative models for water

[Dmitri Dubov]

On Tue, 29 Apr 2008 16:49:24 +0200
  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Dmitri Dubov wrote:
>> Dear David,
>> 
>> Thanks for your short but instructive reply. Now I've 
>>start the 
>> simulation with your SW-model and see that it runs 
>>tenfold slower than 
>> analogues simulation with non-polarizative TIP4P water 
>>cluster.  An 
>> energy minimization of the shell particle positions is 
>>so 
>> time-consuming, isn't it? How can I minimize the energy 
>>only at every 
>> Nth step?
>> 
> You can not. However you could give the shell particle a 
>small mass, make it a normal particle and then run normal 
>MD. You would have to recheck the properties though.
> 
Yes, I see. Should I apply in this case a low temperature 
(~1 K) to D-S relative motion? I do not quite understand 
how could it be done...

> I would not recommend this model for production though. 
>The model by Lamoureux et al. is equally simple but has 
>better properties.
> 
Unfortunately, SSWM4-DP model has only rigid version, and 
I need flexible one. Maybe I am wrong?

Sincerely,
Dmitri
  -----------------------------------------------------------
>> On Mon, 28 Apr 2008 10:49:38 +0200
>>  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>> Dmitri Dubov wrote:
>>>> (for David van der Spoel, imho)
>>>>
>>>> Dear David,
>>>>
>>>> I am doing some similations of large water cluster with 
>>>>tip4p 
>>>> flexible model. I would like to include polarizability 
>>>>effect in the 
>>>> simulation, but trying it get twofold problem.
>>>>
>>>> First, I need the input gro-file with dummy and shell 
>>>>particles. I 
>>>> failed to apply your utility "mkyaw" to my 
>>>>tip4p-structure file 
>>>> directly, since it remained in final file virtual sites 
>>>>MW. Then I 
>>>> reduced my tip4 structure to spc and generated correct 
>>>>gro-file with 
>>>> dummy and shell and without virtuals MW. But! I see that 
>>>>coordinates 
>>>> of both dummy and shell particles coincide with oxygen 
>>>>atoms! Is it 
>>>> acceptable or the result of some mistake of mine?
>>>>
>>>> I cannot examine this (and it is the second problem), 
>>>>since I don't 
>>>> understand how topology file should be generated. I find 
>>>>here the 
>>>> instruction "to use sw.itp instead of spc.itp". But 
>>>>formal 
>>>> replacement in pdb2gmx option "-water" is impossible. 
>>>>Should I
>>>> #include "sw.itp"
>>>> into top-file manually? Is it enough? Could you give me 
>>>>more detailed 
>>>> instructions?
>>>>
>>>> And the last question. As I know at least three 
>>>>polarizative models 
>>>> of water are implemented in GMX. The sw.itp file with 
>>>>your 
>>>> parametrization is in GROMACS distributives, the file of 
>>>>parameters 
>>>> for Roux group's model can be found in gmx-users 
>>>>archive. What about 
>>>> the third model (I mean the model of Gunsteren group)? 
>>>>Is it possible 
>>>> to get their parameter file?
>>>>
>>>
>>> You can easily make it yourself. Read chapter 5 in the 
>>>manual and read 
>>> the paper carefully.
>>>
>>> For mkyaw you should check the extra flags (mkyaw -h).
>>>
>>> You don't need pdb2gmx anywhere for water clusters.
>>>
>>>
>>>> Thank you in advance
>>>>
>>>> Sincerely,
>>>> Dmitri
>>>>
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>>>
>>>
>>> -- 
>>> David van der Spoel, Ph.D.
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., 
>>>Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. 
>>>Fax: +4618511755.
>>> spoel at xray.bmc.uu.se    spoel at gromacs.org 
>>> http://folding.bmc.uu.se
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>> 
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> 
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular 
>Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org 
>  http://folding.bmc.uu.se
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